The design of transition pathways for sustainable electricity systems with high penetrations of renewable energy sources requires the use of energy modeling tools that are able to account for two key aspects: the evolution of fossil fuels and technology prices, and the natural dynamics of renewable resources. However, the modeling methodologies most currently used focus on only one of these two aspects, which hinders their suitability for performing long-term analysis with high penetrations of renewable energy sources. This paper presents a modeling framework that is able to optimize the investment in new renewable generation capacity on the long-term while taking into account the hourly dynamics of electricity supply and demand. The framework combines two of the most used energy planning tools, each able to account for one of the aspects of the modeling of energy systems. The framework was applied to continental Portugal for the time period of 2005–2050, in order to identify optimal investment plans in new renewable and fossil generation capacity with the goal of achieving significant CO2 emissions reduction, under different scenarios. The results show that the inclusion of dynamics in the modeling methodology can help avoid overinvestment and reduce the excess of electricity from renewable energy sources that cannot be used by the system. These results can have a significant impact on the design of a sustainable electricity system and may lead to a diversification of the energy sources used.